Hello all,
I try to install AMBER18 using gnu and intel compiler, but both encountered errors.
The gcc, g++, gfortran version are 4.8.5, and the installation process:
cd ~/amber18
./configure gnu
the configure file has no error.
"No patches available
AMBER_PREFIX=/public/home/test/amber18
AMBER_SOURCE=/public/home/test/amber18
Using the AmberTools miniconda installation in /public/home/test/amber18/miniconda
version 2.7.13
Obtaining the gnu compiler suite versions, e.g.:
gcc -v
The C version is 4.8.5
The Fortran version is 4.8.5
Testing the gcc compiler:
gcc -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o testp testp.c
OK
Testing the g++ compiler:
g++ -fPIC -o testp testp.cpp
OK
Testing the gfortran compiler:
gfortran -fPIC -O0 -o testp testp.f
OK
Testing mixed C/Fortran compilation:
gcc -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -c -o testp.c.o testp.c
gfortran -fPIC -O0 -c -o testp.f.o testp.f
gcc -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o testp testp.c.o testp.f.o -lgfortran -w
OK
Testing pointer size:
gcc -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o test_pointer_size test_pointer_size.c
Detected 64 bit operating system.
Testing flex: OK
Checking NetCDF...
Using bundled NetCDF library.
Using existing NetCDF in '/public/home/test/amber18'
Checking for zlib: OK
Checking for libbz2: OK
Testing the g++ compiler with boost:
g++ -fPIC testp.cpp -lboost_thread -lboost_system -o testp
OK
Configuring fftw-3.3 (may be time-consuming)...
fftw-3.3 configure succeeded.
Configuring XBLAS (may be time-consuming)...
XBLAS configure succeeded.
Configuring CPPTRAJ...complete.
The configuration file, config.h, was successfully created."
Then,
source amber.sh
make install
The installation failed, the information:
/public/home/test/amber18/lib/libfftw3.a(vrank3-transpose.o): In function `apply_cut':
vrank3-transpose.c:(.text+0x5f7): undefined reference to `_intel_fast_memmove'
vrank3-transpose.c:(.text+0x661): undefined reference to `_intel_fast_memcpy'
vrank3-transpose.c:(.text+0x6b9): undefined reference to `_intel_fast_memcpy'
vrank3-transpose.c:(.text+0x748): undefined reference to `_intel_fast_memmove'
vrank3-transpose.c:(.text+0x803): undefined reference to `_intel_fast_memcpy'
/public/home/test/amber18/lib/libfftw3.a(vrank3-transpose.o): In function `apply_toms513':
vrank3-transpose.c:(.text+0xf10): undefined reference to `_intel_fast_memset'
vrank3-transpose.c:(.text+0x1017): undefined reference to `_intel_fast_memcpy'
vrank3-transpose.c:(.text+0x1037): undefined reference to `_intel_fast_memcpy'
vrank3-transpose.c:(.text+0x1151): undefined reference to `_intel_fast_memcpy'
vrank3-transpose.c:(.text+0x117b): undefined reference to `_intel_fast_memcpy'
vrank3-transpose.c:(.text+0x120c): undefined reference to `_intel_fast_memcpy'
/public/home/test/amber18/lib/libfftw3.a(vrank3-transpose.o):vrank3-transpose.c:(.text+0x1227): more undefined references to `_intel_fast_memcpy' follow
collect2: error: ld returned 1 exit status
make[2]: *** [/public/home/test/amber18/bin/sander] Error 1
make[2]: Leaving directory `/public/home/test/amber18/AmberTools/src/sander'
make[1]: *** [serial] Error 2
make[1]: Leaving directory `/public/home/test/amber18/AmberTools/src'
make: *** [install] Error 2
I do not find any useful information from internet, what should I do to solve the problem ?
The intel compiler also has problem
Based on the intel compiler, I have installed AMBER18 successfully.
But it failed to work. I tested the MMPBSA.py.MPI
and the errors:
"ibv_exp_query_device: invalid comp_mask !!! (comp_mask = 0xffffffffffffffff valid_mask = 0x3)
[comput10][[9043,1],0][btl_openib_component.c:1648:init_one_device] error obtaining device attributes for mlx4_0 errno says Invalid argument
ibv_exp_query_device: invalid comp_mask !!! (comp_mask = 0xffffffffffffffff valid_mask = 0x3)
[comput10][[9043,1],2][btl_openib_component.c:1648:init_one_device] error obtaining device attributes for mlx4_0 errno says Invalid argument
ibv_exp_query_device: invalid comp_mask !!! (comp_mask = 0xffffffffffffffff valid_mask = 0x3)
[comput10][[9043,1],3][btl_openib_component.c:1648:init_one_device] error obtaining device attributes for mlx4_0 errno says Invalid argument
ibv_exp_query_device: invalid comp_mask !!! (comp_mask = 0xffffffffffffffff valid_mask = 0x3)
[comput10][[9043,1],1][btl_openib_component.c:1648:init_one_device] error obtaining device attributes for mlx4_0 errno says Invalid argument
/public/home/test/amber18/lib/python2.7/site-packages/MMPBSA_mods/make_trajs.py:631: UserWarning: Solvated topology 0 has IFBOX == 0
warn('Solvated topology %s has IFBOX == 0' % ifbox)
[comput10:32028] 3 more processes have sent help message help-mpi-btl-openib.txt / error in device init
[comput10:32028] Set MCA parameter "orte_base_help_aggregate" to 0 to see all help / error messages
forrtl: severe (168): Program Exception - illegal instruction
Image PC Routine Line Source
libifcoremt.so.5 00002B052A7D8575 for__signal_handl Unknown Unknown
libpthread-2.17.s 00002B052B57F5D0 Unknown Unknown Unknown
sander 000000000060A060 init_timers_ Unknown Unknown
sander 00000000004F4A09 sander_ Unknown Unknown
sander 00000000004F48E2 MAIN__ Unknown Unknown
sander 000000000046CAEE main Unknown Unknown
libc-2.17.so 00002B052B7AE3D5 __libc_start_main Unknown Unknown
sander 000000000046C9F9 Unknown Unknown Unknown
forrtl: severe (168): Program Exception - illegal instruction
Image PC Routine Line Source
libifcoremt.so.5 00002B79AA6E2575 for__signal_handl Unknown Unknown
libpthread-2.17.s 00002B79AB4895D0 Unknown Unknown Unknown
sander 000000000060A060 init_timers_ Unknown Unknown
sander 00000000004F4A09 sander_ Unknown Unknown
sander 00000000004F48E2 MAIN__ Unknown Unknown
sander 000000000046CAEE main Unknown Unknown
Image PC Routine Line Source
libifcoremt.so.5 00002AFA70111575 for__signal_handl Unknown Unknown
libpthread-2.17.s 00002AFA70EB85D0 Unknown Unknown Unknown
sander 000000000060A060 init_timers_ Unknown Unknown
sander 00000000004F4A09 sander_ Unknown Unknown
sander 00000000004F48E2 MAIN__ Unknown Unknown
sander 000000000046CAEE main Unknown Unknown
libc-2.17.so 00002AFA710E73D5 __libc_start_main Unknown Unknown
sander 000000000046C9F9 Unknown Unknown Unknown
forrtl: severe (168): Program Exception - illegal instruction
Image PC Routine Line Source
libifcoremt.so.5 00002AB59055A575 for__signal_handl Unknown Unknown
libpthread-2.17.s 00002AB5913015D0 Unknown Unknown Unknown
sander 000000000060A060 init_timers_ Unknown Unknown
sander 00000000004F4A09 sander_ Unknown Unknown
sander 00000000004F48E2 MAIN__ Unknown Unknown
sander 000000000046CAEE main Unknown Unknown
libc-2.17.so 00002AB5915303D5 __libc_start_main Unknown Unknown
sander 000000000046C9F9 Unknown Unknown Unknown
File "/public/home/test/amber18/bin/MMPBSA.py.MPI", line 100, in <module>
File "/public/home/test/amber18/bin/MMPBSA.py.MPI", line 100, in <module>
File "/public/home/test/amber18/bin/MMPBSA.py.MPI", line 100, in <module>
File "/public/home/test/amber18/bin/MMPBSA.py.MPI", line 100, in <module>
app.run_mmpbsa()
File "/public/home/test/amber18/lib/python2.7/site-packages/MMPBSA_mods/main.py", line 218, in run_mmpbsa
app.run_mmpbsa()
File "/public/home/test/amber18/lib/python2.7/site-packages/MMPBSA_mods/main.py", line 218, in run_mmpbsa
app.run_mmpbsa()
File "/public/home/test/amber18/lib/python2.7/site-packages/MMPBSA_mods/main.py", line 218, in run_mmpbsa
app.run_mmpbsa()
File "/public/home/test/amber18/lib/python2.7/site-packages/MMPBSA_mods/main.py", line 218, in run_mmpbsa
self.calc_list.run(rank, self.stdout)
File "/public/home/test/amber18/lib/python2.7/site-packages/MMPBSA_mods/calculation.py", line 82, in run
self.calc_list.run(rank, self.stdout)
File "/public/home/test/amber18/lib/python2.7/site-packages/MMPBSA_mods/calculation.py", line 82, in run
self.calc_list.run(rank, self.stdout)
File "/public/home/test/amber18/lib/python2.7/site-packages/MMPBSA_mods/calculation.py", line 82, in run
self.calc_list.run(rank, self.stdout)
File "/public/home/test/amber18/lib/python2.7/site-packages/MMPBSA_mods/calculation.py", line 82, in run
calc.run(rank, stdout=stdout, stderr=stderr)
File "/public/home/test/amber18/lib/python2.7/site-packages/MMPBSA_mods/calculation.py", line 82, in run
calc.run(rank, stdout=stdout, stderr=stderr)
File "/public/home/test/amber18/lib/python2.7/site-packages/MMPBSA_mods/calculation.py", line 157, in run
calc.run(rank, stdout=stdout, stderr=stderr)
File "/public/home/test/amber18/lib/python2.7/site-packages/MMPBSA_mods/calculation.py", line 157, in run
calc.run(rank, stdout=stdout, stderr=stderr)
File "/public/home/test/amber18/lib/python2.7/site-packages/MMPBSA_mods/calculation.py", line 157, in run
calc.run(rank, stdout=stdout, stderr=stderr)
File "/public/home/test/amber18/lib/python2.7/site-packages/MMPBSA_mods/calculation.py", line 157, in run
self.prmtop))
self.prmtop))
CalcError: /public/home/test/amber18/bin/sander failed with prmtop ../../../../07-topX3/gper1-g1.prmtop!
CalcError: /public/home/test/amber18/bin/sander failed with prmtop ../../../../07-topX3/gper1-g1.prmtop!
self.prmtop))
self.prmtop))
Error occured on rank 3.
Exiting. All files have been retained.
Error occured on rank 1.
Exiting. All files have been retained.
CalcError: /public/home/test/amber18/bin/sander failed with prmtop ../../../../07-topX3/gper1-g1.prmtop!
CalcError: /public/home/test/amber18/bin/sander failed with prmtop ../../../../07-topX3/gper1-g1.prmtop!
Error occured on rank 2.
Exiting. All files have been retained.
Error occured on rank 0.
Exiting. All files have been retained.
[comput10:32028] 3 more processes have sent help message help-mpi-api.txt / mpi-abort"
The installation of Amber16 also have similar problems.
The operating system is centos 7.6.
I have yum gcc gcc-gfortran gcc-c++ flex tcsh zlib-devel \
bzip2-devel libXt-devel libXext-devel libXdmcp-devel tkinter \
openmpi perl perl-ExtUtils-MakeMaker patch bison
the yum can not install openmpi-devel, thus I installed the openmpi based on gnu and intel compiler.
So I am confused about what the problem is.
Best regards
Qiao Xue
xmgign.126.com
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Received on Tue Sep 03 2019 - 01:00:02 PDT
